Top Tweets for #DeepTree
Our #DeepTree🌳 paper got accepted to @FrontiersIn🎉 = the best gift🎁 to celebrate the *exact* 7-year anniversary of my 1st day at uni!🎊
Enjoy the read of our #BioImage #Analysis approach🔬 to #SingleCell lineaging🧫 now in @FrontComputSci & in the 🧵👇: https://t.co/Grth05hrkZ
#DeepTree 🌳 cont'd 🧵:
Our #Cell #Tracking package📦 got recently updated to #version 0.4.2 + we have a new logo!👇
Bring #btrack to your #Microscopy & #DataAnalysis community by sharing your thoughts (❤️) & don't forget to ⭐ @quantumjot's GitHub repo:
🔗https://t.co/9eomMevev5
#Free2Read and in latest volume of Journal of Science Education and Technology, @SpringerEdu:
Zooming in Time—Exploring Students’ Interpretations of a Dynamic Tree of Life (@JorgenStenlund, @DrBlazar, L., Tibell). https://t.co/NEM7tnHHBw
#DeepTree #EvolutionaryTimeScales
'I’m happy to say that our (mine, @DrBlazar & L.Tibell),latest research “Zooming in #Time #Exploring Student's #Interpretations of a #Dynamic Tree of Life is published in #JOST. Read and share here https://t.co/xwJqbgvtXV
@SpringerEdu #OpenAccess #deeptime #evolution #DeepTree
@SaraAWatson Thanks for RTing our work!🙏 Super-interested folks may want to keep an eye👀 on the #DeepTree🌳 hashtag for more updates explaining our work & example datasets!🖥️ More to be found on my @github repository - 🔗 link attached below👇
https://t.co/WzQtkapqh9
https://t.co/AsLRtm8n1Y
#DeepTree🌳(1/🧵):
I'm beyond thrilled🤩 to announce that my 1️⃣st ever first-author preprint📄 is finally out on @biorxivpreprint!🎉
Enjoy reading my #PhD #project contribution👩💻 to Lowe & Charras #research teams to reconstruct #Deep #SingleCell #Lineages🔬https://t.co/l2ye39yZlG
Welcome to @SpaceConscious - Kristina Ulicna
@KristinaUlicna
PhD studentWoman scientist
@LIDo_DTP & @UCL
behind #DeepTree #projectDeciduous Into #DeepLearningWoman technologist #SingleCell #TrackingPetri #CancerBiologyMicroscope & #CellCycle
UC London UK https://t.co/yHueroAfJx
@JanaLalakova Thanks for retweeting our work!🙏 Super-interested folks may want to keep an eye👀 on the #DeepTree🌳 hashtag for more details about what we (and you!👊) can do with our single-cell #tracking software🖥️ More to be found on my @github repository's link 🔗👇
https://t.co/WzQtkapqh9
#DeepTree🌳(18/🧵):
What sort of computational biologists would we even be👩💻👨💻 if we didn't incorporate #DeepLearning into our #bioimage analysis pipeline? Check out our team's experience in training #MachineLearning models for microscopy data annotation🔬
https://t.co/OGinHQOQqu
Oh look 👀: My recent talk about my #PhD #research #project 👩💻 sparked some interest ✨ in #BioImaging & #DeepLearning enthusiasts! Check out the elegant summary 🙏 of my slides in @tomlincr's 🧵& learn more about what we (& you! 👊) can do with #MachineLearning in biosciences 🧫
My #DeepTree🌳 work got RT'd by “Promising Preprints” @PromPreprint: “A bot tweeting @biorxivpreprint publications reaching the top 10% @altmetric score within their 1️⃣st month after publication” & that totally made all the lockdown pain & effort feel worth it!😌 @AcademicChatter
#DeepTree🌳(17/🧵):
Evidence of coolness #3: #Arboretum self-identifies cell tracking errors⚠️ Check my cell categorisation into SURVIVOR (cyan; correct), INCOMER (gold; migrated into view) & MISTRACKED (red; error) group using interactive colour-coding🎨 https://t.co/2RGOVzvzfK
#DeepTree🌳(16/🧵):
Evidence of coolness #2: #Arboretum allows you to shortlist individual cells & put them in the context of its lineage tree🌳 The previously boxed cell was in frame #994 = its lineage was imaged for ~66hrs⌛. It's about to divide soon👩👧👧!
https://t.co/D6heeG76dK
#DeepTree🌳(15/🧵):
Evidence of coolness #1: #Arboretum allows you to visualise each segmented cell (=nucleus) trajectory in real-time⌛ using a visually appealing colour palette based on cell ID, parent ID, root ID, phase label, cell fate & much more...📈
https://t.co/D6heeG76dK
#DeepTree🌳(14/🧵):
To visualise the #bTrack pipeline, we (@quantumjot🙌) developed the #Arboretum software 🌳🌳🌳 for real-time feedback between lineage tree analysis, cell tracking & image data with @napari_imaging🔬 Coolest for-biologist plugin ever! 📸
https://t.co/D6heeG76dK
#DeepTree🌳(13/🧵):
We (@quantumjot🙌) developed #bTrack to follow single-cell trajectories👣& assign parent cell to its children upon division ➡️ #bTrack reconstructs these relationships to track cell division history for multiple generations. Cool huh?😎
https://t.co/D6heeG76dK
#DeepTree🌳(12/🧵):
Per-frame cell #segmentation & #classification provides information for cell #tracking = connecting single cell observations in space & time👣. This way, you can reconstruct fully annotated cell lineage trees🌳 in fully automated manner
https://t.co/D6heeG76dK
#DeepTree🌳(11/🧵):
For each cell in the image, you need to determine its position📍 & label its mitotic phase. In our dataset comprising >250,000 single cells🧫, manual annotation is not an option ➡️ #DeepLearning saves your life & automates both tasks!🖥️
https://t.co/D6heeG76dK
#DeepTree🌳(10/🧵):
Turns out, lots of #fluorescence #microscopy's got your back!🔬 We acquired 44 long-term (>80hrs) time-lapse movies🎥 of cultured MDCK cells with 2 channels(💡&🦠) But such quantity of cell #imaging data requires post-processing tools🖥️
https://t.co/D6heeG76dK
#DeepTree🌳(9/🧵):
How do you gain the single-cell data for such robust analysis?📊 We combined our #wetlab & #drylab expertise to computationally digest #timelapse #microscopy datasets🔬 to detect & track single cells using our custom-developed software🖥️
https://t.co/D6heeG76dK
#DeepTree🌳(8/🧵):
We analysed cycling correlations between cell family members on the ancestral (mother, grandma...) & side branches (sister, cousin...) in high-replicate (>5000) deep (8-geners) extended (4th-cousin) lineage trees of >20000 single cells🌳
https://t.co/D6heeG76dK
#DeepTree🌳(7/🧵):
How is cell cycling heterogeneity established & propagated❓ Is cycle time heritable across generations (resembles parent's time) or is it liberated from any instilled parent's control (lasts longer/shorter)? Or a combination of both?😮
https://t.co/D6heeG76dK
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